A) A phrase that seems to simply state the obvious but actually implies helplessness.

B) A phrase that seems to simply state the obvious but actually means "it will be what it is," as in "it ain't gonna change, so deal with it or don't." See also tough shit, oh well, cry me a river and tfb.

Meaning A
J: I can't believe the price of gas!

B: It is what it is.

Meaning B
J: It troubles me that you continue to put cyanide in my Yoohoo even after I've asked you to stop.